Insulin resistance is predictive of the development of non-insulin- dependent diabetes mellitus in Pima Indians, and this abnormality is associated with decreased rates of glycogen synthesis in skeletal muscle and of its regulatory enzyme complex, the glycogen-bound type protein phosphatase (PP1). Glycogen-associated PP1 activity is determined by an isoform of the catalytic subunit complexed with the glycogen-targeting regulatory subunit, and structural alterations of either component could result in the biochemical abnormalities observed in insulin resistant Pimas. Three genetically distinct PP1 catalytic subunit isoforms are known (PP1 alpha, PP1 beta, and PP1 gamma). We have previously determined the exon-intron structure of the genes coding for PP1 alpha catalytic subunit (PPP1CA; 7 exons), PP1 beta (PPP1CB, 8 exons), PP1 gamma (PPP1CC, 7 exons), and PP1 regulatory G-subunit (PPP1R3, 4 exons), and we also positioned PPP1R3 on chromosome 7q. We have isolated polymorphic repeat markers at all PPP1 genes, and so far we have analyzed markers at PPP1CA, PPP1CB and PPP1R3. In contrast to PPP1Ca and PPP1Cb, we found a significant linkage and association of PPP1R3 with parameters of insulin action and NIDDM. Using direct sequencing of PPP1R3, we detected an amino acid substitution and codon 883 (Arg --> Ser) and codon 905 (Asp --> Tyr), and found that both variants are associated with higher insulin action and lower prevalence of NIDDM. Experiments are in progress to determine the functional significance of the amino acid substitutions in PPP1R3. Furthermore, we are also comparing the mRNA levels in skeletal muscle biopsies from insulin-sensitive and insulin-resistant Pima Indians.